+Open data
-Basic information
Entry | Database: PDB / ID: 1pvw | ||||||
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Title | 3,4-dihydroxy-2-butanone 4-phosphate synthase from M. jannaschii | ||||||
Components | 3,4-dihydroxy-2-butanone 4-phosphate synthase | ||||||
Keywords | ISOMERASE / riboflavin biosynthesis | ||||||
Function / homology | Function and homology information 3,4-dihydroxy-2-butanone-4-phosphate synthase / 3,4-dihydroxy-2-butanone-4-phosphate synthase activity / riboflavin biosynthetic process / manganese ion binding / magnesium ion binding / cytosol Similarity search - Function | ||||||
Biological species | Methanocaldococcus jannaschii (archaea) | ||||||
Method | X-RAY DIFFRACTION / MIR / Resolution: 2.45 Å | ||||||
Authors | Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M. | ||||||
Citation | Journal: J.Biol.Chem. / Year: 2003 Title: Structure of 3,4-Dihydroxy-2-butanone 4-Phosphate Synthase from Methanococcus jannaschii in Complex with Divalent Metal Ions and the Substrate Ribulose 5-Phosphate: IMPLICATIONS FOR THE CATALYTIC MECHANISM Authors: Steinbacher, S. / Schiffmann, S. / Richter, G. / Huber, R. / Bacher, A. / Fischer, M. #1: Journal: J.Biol.Chem. / Year: 2002 Title: Biosynthesis of Riboflavin in Archaea Studies on the Mechanism of 3,4-Dihydroxy-2-butanone-4-phosphate Synthase of Methanococcus jannaschii Authors: Fischer, M. / Romisch, W. / Schiffmann, S. / Kelly, M. / Oschkinat, H. / Steinbacher, S. / Huber, R. / Eisenreich, W. / Richter, G. / Bacher, A. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 1pvw.cif.gz | 138.8 KB | Display | PDBx/mmCIF format |
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PDB format | pdb1pvw.ent.gz | 110 KB | Display | PDB format |
PDBx/mmJSON format | 1pvw.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Summary document | 1pvw_validation.pdf.gz | 454.1 KB | Display | wwPDB validaton report |
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Full document | 1pvw_full_validation.pdf.gz | 463.1 KB | Display | |
Data in XML | 1pvw_validation.xml.gz | 24.3 KB | Display | |
Data in CIF | 1pvw_validation.cif.gz | 32.6 KB | Display | |
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/pv/1pvw ftp://data.pdbj.org/pub/pdb/validation_reports/pv/1pvw | HTTPS FTP |
-Related structure data
-Links
-Assembly
Deposited unit |
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1 |
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2 |
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3 |
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Unit cell |
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Details | dimer; the asymmeric unit contains a dimer, representing the biological assembly and a monomer fro which the second monomer is generated by a twofold axis |
-Components
#1: Protein | Mass: 25832.621 Da / Num. of mol.: 3 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Methanocaldococcus jannaschii (archaea) Gene: MJ0055 / Plasmid: pNCO-MJ / Production host: Escherichia coli (E. coli) / Strain (production host): XL1 References: UniProt: Q60364, Isomerases; Intramolecular transferases; Transferring other groups #2: Chemical | #3: Chemical | ChemComp-CA / | #4: Chemical | ChemComp-PO4 / | #5: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.32 Å3/Da / Density % sol: 46.66 % |
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Crystal grow | Temperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.5 Details: PEG1000, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K |
Crystal grow | *PLUS Method: unknown / Details: Fischer, M., (2002) J. Biol. Chem., 277, 41410. |
-Data collection
Diffraction | Mean temperature: 287 K |
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Diffraction source | Source: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.548 Å |
Detector | Type: MARRESEARCH / Detector: IMAGE PLATE / Date: Jan 12, 2001 / Details: Osmic |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1.548 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→20 Å / Num. all: 24943 / Num. obs: 24943 / % possible obs: 97.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.7 % / Rmerge(I) obs: 0.065 / Net I/σ(I): 21.5 |
Reflection shell | Resolution: 2.45→2.54 Å / Rmerge(I) obs: 0.295 / Mean I/σ(I) obs: 3.5 / % possible all: 97.3 |
Reflection shell | *PLUS % possible obs: 97.3 % |
-Processing
Software |
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Refinement | Method to determine structure: MIR / Resolution: 2.45→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
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Refinement step | Cycle: LAST / Resolution: 2.45→20 Å
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Refine LS restraints |
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Refinement | *PLUS Lowest resolution: 20 Å | |||||||||||||||||||||||||
Solvent computation | *PLUS | |||||||||||||||||||||||||
Displacement parameters | *PLUS |